Hmm. I'm not sure I agree, noble. He is protecting Buffy, but it's still pretty dark - and he doesn't do it in hot blood, he explains it then smothers him. He's also Ripper.
I'm really sad they never did a Giles spin-off - though I can imagine it would actually have turned out terrible
- because it would have been great. I love how his character goes from fuddy-duddy harmless librarian to kick-arse. I think it is also a really good illustration of how your perspective shifts - we're made to think he is really middle-aged in the early bits, and he seems to get younger as the series goes on, which I assume is to do with Buffy and the others recognising he's actually just another fallible adult who hasn't worked out all the answers yet.
But the darkest bit IMO is the bit where he is drugging Buffy and hypnotising her (another bit of classic Whedon 'fucking with a woman's mind and subjecting her to violence' where he's really showing how nasty the trope is). He ends up rejecting the Council, but it shows you how conflicted he is.
noble - no, true, I don't think it's condoning them either, but it's the way these themes run through his work, as if he can't figure out how to write a female character who isn't going to be subjected to something along these lines. It could be he's fascinated by broken women and wants to understand, but I'd still suggest there's something invasive about that, and certainly there's something worrying in the way he does it over and over.